On my MySQL installation 5.5.31-0+wheezy1-log (Debian)
The query regarding the custom var aggregation are using thw wrong index.
Here the Explain https://gist.github.com/RoyBellingan/9170698
The choosen index is a three column index idsite config_id visit_last_action_time
If a "hint" to use the index_idsite_datetime (two column), a very good improvement can be seen.
I'm not sure if this is a bug. My guess is that you don't have enough rows in the table. I believe if you had more rows in your table, the query optimizer would pick the right index. Could you try run the same query on 10 or even 100 times more data?
Is not a bug, just a performance improvement in reality...
The log_visit is around 1M rows
I've rerunned it now, increasing the time span log_visit.visit_last_action_time >= '2014-02-10 23:00:00' AND log_visit.visit_last_action_time <= '2014-02-24 22:59:59'
Explain again suggest to use index_idsite_config_datetime, this time rows count is around 540K.